[med-svn] r1181 - in trunk/packages/emboss/trunk/debian: . patches

[charles-guest at alioth.debian.org]

Author: charles-guest
Date: 2008-01-20 23:43:36 +0000 (Sun, 20 Jan 2008)
New Revision: 1181

Added:
   trunk/packages/emboss/trunk/debian/patches/embindex-fix-2008-01-19.patch
Modified:
   trunk/packages/emboss/trunk/debian/changelog
   trunk/packages/emboss/trunk/debian/patches/series
Log:
Official fix number 3

Modified: trunk/packages/emboss/trunk/debian/changelog
===================================================================
--- trunk/packages/emboss/trunk/debian/changelog	2008-01-20 19:43:17 UTC (rev 1180)
+++ trunk/packages/emboss/trunk/debian/changelog	2008-01-20 23:43:36 UTC (rev 1181)
@@ -6,11 +6,15 @@
     - debian/emboss.sharedmimeinfo describes the ABIF format of the .ab1 files.
     - debian/abiview.desktop associates `abiview' with chromatograms in ABIF
       format via the application/ab1 and application/x-dna formats.
-  * debian/patches/using-pager-in-tfm.patch:
-    Patching tfm so that it uses the alternatives system `/usr/bin/pager' if
-    the `PAGER' environment variable is not defined.
+  * debian/patches:
+    - using-pager-in-tfm.patch:
+      Patching tfm so that it uses the alternatives system `/usr/bin/pager' if
+      the `PAGER' environment variable is not defined.
+    - embindex-fix-2008-01-19.patch:
+      Official fix 3. EMBOSS-5.0.0/nucleus/embindex.c 18 Jan 2008.
+      Order and fill fixes to sort out potential problems with kw/de/tx indexes.
 
- -- Charles Plessy <charles-debian-nospam at plessy.org>  Fri, 18 Jan 2008 14:29:05 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Mon, 21 Jan 2008 08:40:14 +0900
 
 emboss (5.0.0-3) unstable; urgency=low
 

Added: trunk/packages/emboss/trunk/debian/patches/embindex-fix-2008-01-19.patch
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/embindex-fix-2008-01-19.patch	                        (rev 0)
+++ trunk/packages/emboss/trunk/debian/patches/embindex-fix-2008-01-19.patch	2008-01-20 23:43:36 UTC (rev 1181)
@@ -0,0 +1,56 @@
+Fix 3. EMBOSS-5.0.0/nucleus/embindex.c
+
+18 Jan 2008: Order and fill fixes to sort out potential problems
+             with kw/de/tx indexes.
+Index: EMBOSS-5.0.0/nucleus/embindex.c
+===================================================================
+--- EMBOSS-5.0.0.orig/nucleus/embindex.c
++++ EMBOSS-5.0.0/nucleus/embindex.c
+@@ -1196,13 +1196,13 @@
+     entry->txorder = (entry->pagesize - 60) / ((entry->txlen + 1) + 12);
+     entry->txfill  = (entry->pagesize - 16) / (entry->txlen + 28);
+ 
+-    entry->kwsecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
+-    entry->desecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
+-    entry->txsecorder = (entry->pagesize - 60) / ((entry->idlen + 1) + 12);
+-
+-    entry->kwsecfill  = (entry->pagesize - 16) / (entry->idlen + 4);
+-    entry->desecfill  = (entry->pagesize - 16) / (entry->idlen + 4);
+-    entry->txsecfill  = (entry->pagesize - 16) / (entry->idlen + 4);
++    entry->kwsecorder = (entry->pagesize - 60) / ((entry->kwlen + 1) + 12);
++    entry->desecorder = (entry->pagesize - 60) / ((entry->delen + 1) + 12);
++    entry->txsecorder = (entry->pagesize - 60) / ((entry->txlen + 1) + 12);
++
++    entry->kwsecfill  = (entry->pagesize - 16) / (entry->kwlen + 4);
++    entry->desecfill  = (entry->pagesize - 16) / (entry->delen + 4);
++    entry->txsecfill  = (entry->pagesize - 16) / (entry->txlen + 4);
+ 
+     entry->idsecorder = (entry->pagesize - 60) / 24;
+     entry->idsecfill  = (entry->pagesize - 60) / 20;
+@@ -1251,7 +1251,7 @@
+ 					     entry->cachesize,
+ 					     entry->idsecorder, slevel,
+ 					     entry->idsecfill, count,
+-					     entry->kwlen);
++					     entry->idlen);
+ 	if(!entry->idcache)
+ 	    ajFatal("Cannot open ID index");
+ 	
+@@ -1267,7 +1267,7 @@
+ 					     entry->cachesize,
+ 					     entry->acsecorder, slevel,
+ 					     entry->acsecfill, count,
+-					     entry->kwlen);
++					     entry->aclen);
+ 	if(!entry->accache)
+ 	    ajFatal("Cannot open ACC index");
+ 
+@@ -1282,7 +1282,7 @@
+ 					     entry->cachesize,
+ 					     entry->svsecorder, slevel,
+ 					     entry->svsecfill, count,
+-					     entry->kwlen);
++					     entry->svlen);
+ 	if(!entry->svcache)
+ 	    ajFatal("Cannot open SV index");
+ 

Modified: trunk/packages/emboss/trunk/debian/patches/series
===================================================================
--- trunk/packages/emboss/trunk/debian/patches/series	2008-01-20 19:43:17 UTC (rev 1180)
+++ trunk/packages/emboss/trunk/debian/patches/series	2008-01-20 23:43:36 UTC (rev 1181)
@@ -1,3 +1,4 @@
+embindex-fix-2008-01-19.patch
 using-pager-in-tfm.patch
 psiphi-fix-2007-07-27.patch
 ajindex-fix-2008-01-09.patch